Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

In mammals, the canonical somatic DNA methylation landscape is established upon specification of the embryo proper and subsequently disrupted within many cancer types(1-4). However, the underlying mechanisms that direct this genome-scale transformation remain elusive, with no clear model for its systematic acquisition or potential developmental utility(5,6). Here we analyzed global remethylation from the mouse preimplantation embryo into the early epiblast and extraembryonic ectoderm. We show that these two states acquire highly divergent genomic distributions with substantial disruption of bimodal, CpG density-dependent methylation in the placental progenitor(7,8). The extraembryonic epigenome includes specific de novo methylation at hundreds of embryonically-protected CpG island promoters particularly those that are associated with key developmental regulators and orthologously methylated across most human cancer types(9). Our data suggest that the evolutionary innovation of extraembryonic tissues may have required cooption of DNA methylation-based suppression as an alternative to the embryonically utilized Polycomb group proteins, which coordinate germlayer formation in response to extraembryonic cues(10). Moreover, we establish that this decision is made deterministically downstream of promiscuously utilized, and frequently oncogenic, signaling pathways via a novel combination of epigenetic cofactors. Methylation of developmental gene promoters during tumorigenesis may therefore reflect the misappropriation of an innate trajectory and the spontaneous reacquisition of a latent, developmentally-encoded epigenetic landscape.